Read Alignment

Variant Calling

Column

Overview

  • GATK4 best practices
  • Site level filtering:
  • bi-allelic SNPs
  • 95% truth sensitivity (VQSR)
  • Genotype level filtering:
  • DP: 4 - 77 (mean DP + 4*SD)
  • GQ >= 20
  • Else missing (./.)

Number of Variants

variable raw site_filtered gt_filtered
TOTAL_SNPS 16,643,754.00 9,115,052.00 5,126,585.00
NUM_IN_DB_SNP 12,117,419.00 8,486,322.00 4,846,921.00
NOVEL_SNPS 4,526,335.00 628,730.00 279,664.00
PCT_DBSNP 0.73 0.93 0.95
DBSNP_TITV 1.94 2.07 2.30
NOVEL_TITV 1.07 1.53 1.82
TOTAL_INDELS 3,454,237.00 0.00 0.00
TOTAL_MULTIALLELIC_SNPS 856,605.00 0.00 0.00

Column

SNPs per sample

Sample metrics

Linie SAMPLE_ALIAS target_cvg HET_HOMVAR_RATIO TOTAL_HET_DEPTH TOTAL_SNPS NUM_IN_DB_SNP NOVEL_SNPS FILTERED_SNPS PCT_DBSNP DBSNP_TITV NOVEL_TITV TOTAL_INDELS NOVEL_INDELS FILTERED_INDELS PCT_DBSNP_INDELS NUM_IN_DB_SNP_INDELS DBSNP_INS_DEL_RATIO NOVEL_INS_DEL_RATIO TOTAL_MULTIALLELIC_SNPS NUM_IN_DB_SNP_MULTIALLELIC TOTAL_COMPLEX_INDELS NUM_IN_DB_SNP_COMPLEX_INDELS SNP_REFERENCE_BIAS NUM_SINGLETONS
DUK H07788 30x 0.193108 13843032 1984239 1948555 35684 0 0.982016 2.271589 1.960591 0 0 0 ? 0 0 0 0 0 0 0 0.505178 65
DUK H07789 30x 0.230014 14312572 1993501 1956434 37067 0 0.981406 2.273841 1.954017 0 0 0 ? 0 0 0 0 0 0 0 0.504956 92
DUK H07790 30x 0.193317 8649822 1996228 1961397 34831 0 0.982552 2.271863 1.888382 0 0 0 ? 0 0 0 0 0 0 0 0.506207 74
DUK H07791 30x 0.166171 9391113 2012670 1975383 37287 0 0.981474 2.261462 1.890241 0 0 0 ? 0 0 0 0 0 0 0 0.507743 108
DUK H07792 30x 0.201879 9876492 1998241 1958297 39944 0 0.980010 2.268928 1.955312 0 0 0 ? 0 0 0 0 0 0 0 0.506036 101
DUK H07793 30x 0.164784 8169416 1925909 1887360 38549 0 0.979984 2.273371 1.956892 0 0 0 ? 0 0 0 0 0 0 0 0.507314 125
DUK H07794 30x 0.195816 9217169 1957825 1922103 35722 0 0.981754 2.267360 1.887560 0 0 0 ? 0 0 0 0 0 0 0 0.507682 116
DUK H07795 30x 0.203880 7919034 2055927 2017391 38536 0 0.981256 2.259629 1.918289 0 0 0 ? 0 0 0 0 0 0 0 0.506481 116
DUK H07796 30x 0.204992 9374049 1996249 1958001 38248 0 0.980840 2.271361 1.906162 0 0 0 ? 0 0 0 0 0 0 0 0.508017 85
DUK H07797 30x 0.225372 8461332 2037813 1999910 37903 0 0.981400 2.261166 1.899556 0 0 0 ? 0 0 0 0 0 0 0 0.506414 94
DUK I34770 5x 0.212805 4202237 1872118 1836581 35537 0 0.981018 2.271617 1.943998 0 0 0 ? 0 0 0 0 0 0 0 0.502603 359
DUK I34771 5x 0.204915 3737893 1807234 1772934 34300 0 0.981021 2.280271 1.909245 0 0 0 ? 0 0 0 0 0 0 0 0.501216 457
DUK I34772 5x 0.420702 1008814 493866 481845 12021 0 0.975659 2.378594 2.018835 0 0 0 ? 0 0 0 0 0 0 0 0.483877 1023
DUK I34773 5x 0.187163 3544032 1786022 1752406 33616 0 0.981178 2.292437 1.922622 0 0 0 ? 0 0 0 0 0 0 0 0.503592 505
DUK I34774 5x 0.321020 1623954 849754 830218 19536 0 0.977010 2.368721 1.955969 0 0 0 ? 0 0 0 0 0 0 0 0.490742 1306
DUK I34775 5x 0.195923 2540813 1516900 1487527 29373 0 0.980636 2.301617 1.933779 0 0 0 ? 0 0 0 0 0 0 0 0.499578 452
DUK I34776 5x 0.196547 2875277 1451680 1422692 28988 0 0.980031 2.334791 1.927785 0 0 0 ? 0 0 0 0 0 0 0 0.502224 1250
DUK I34777 5x 0.222054 3394582 1688025 1654597 33428 0 0.980197 2.294002 1.958754 0 0 0 ? 0 0 0 0 0 0 0 0.501252 602
DUK I34778 5x 0.276850 3421077 1549234 1517886 31348 0 0.979765 2.308794 1.946518 0 0 0 ? 0 0 0 0 0 0 0 0.499637 1118
DUK I34779 5x 0.204549 3315333 1708789 1674518 34271 0 0.979944 2.294829 1.912715 0 0 0 ? 0 0 0 0 0 0 0 0.500896 820
DUK I34780 5x 0.211713 4582506 1883370 1849364 34006 0 0.981944 2.275965 1.905006 0 0 0 ? 0 0 0 0 0 0 0 0.503507 475
DUK I34781 5x 0.183519 2703516 1596308 1565007 31301 0 0.980392 2.301703 1.923142 0 0 0 ? 0 0 0 0 0 0 0 0.500308 836
DUK I34782 5x 0.223184 3125949 1629008 1596833 32175 0 0.980249 2.294681 1.933266 0 0 0 ? 0 0 0 0 0 0 0 0.498060 421
DUK I34783 5x 0.228496 3366351 1646831 1615093 31738 0 0.980728 2.289502 1.928670 0 0 0 ? 0 0 0 0 0 0 0 0.501269 1020
DUK I34784 5x 0.275089 3008179 1393505 1366100 27405 0 0.980334 2.322510 1.902457 0 0 0 ? 0 0 0 0 0 0 0 0.498359 1186
DUC H07758 30x 0.127951 6588794 2100074 2059647 40427 0 0.980750 2.268233 1.884758 0 0 0 ? 0 0 0 0 0 0 0 0.508311 101
DUC H07759 30x 0.162971 6457986 2162126 2119578 42548 0 0.980321 2.270005 1.871566 0 0 0 ? 0 0 0 0 0 0 0 0.507736 143
DUC H07760 30x 0.150750 8132832 2149544 2106966 42578 0 0.980192 2.271463 1.891545 0 0 0 ? 0 0 0 0 0 0 0 0.508154 119
DUC H07761 30x 0.170101 7884641 2150025 2106790 43235 0 0.979891 2.276674 1.915178 0 0 0 ? 0 0 0 0 0 0 0 0.508087 88
DUC H07762 30x 0.162103 9458716 2138775 2095693 43082 0 0.979857 2.277614 1.910946 0 0 0 ? 0 0 0 0 0 0 0 0.506580 105
DUC H07763 30x 0.160885 9944922 2110024 2068917 41107 0 0.980518 2.282989 1.897512 0 0 0 ? 0 0 0 0 0 0 0 0.502476 79
DUC H07764 30x 0.148103 9039938 2141621 2099896 41725 0 0.980517 2.275529 1.920896 0 0 0 ? 0 0 0 0 0 0 0 0.506702 84
DUC H07765 30x 0.622541 25008545 2231911 2188027 43884 0 0.980338 2.274215 1.892052 0 0 0 ? 0 0 0 0 0 0 0 0.472609 94
DUC H07766 30x 0.169709 7726999 2181497 2136887 44610 0 0.979551 2.277102 1.904675 0 0 0 ? 0 0 0 0 0 0 0 0.507936 102
DUC H07767 30x 0.185156 9100502 2075787 2036043 39744 0 0.980853 2.274829 1.881044 0 0 0 ? 0 0 0 0 0 0 0 0.486300 104
DUC I34755 5x 0.195965 1924614 1319092 1291673 27419 0 0.979214 2.294219 1.881055 0 0 0 ? 0 0 0 0 0 0 0 0.495421 290
DUC I34756 5x 0.159771 3809528 2043270 2004645 38625 0 0.981097 2.286891 1.888282 0 0 0 ? 0 0 0 0 0 0 0 0.504812 184
DUC I34757 5x 0.180106 2433182 1587799 1555164 32635 0 0.979446 2.309303 1.951791 0 0 0 ? 0 0 0 0 0 0 0 0.500217 509
DUC I34758 5x 0.231745 2491121 1450455 1421571 28884 0 0.980086 2.304158 1.907297 0 0 0 ? 0 0 0 0 0 0 0 0.497620 338
DUC I34759 5x 0.224300 2656400 1526533 1493753 32780 0 0.978527 2.309757 1.909123 0 0 0 ? 0 0 0 0 0 0 0 0.497635 514
DUC I34760 5x 0.213459 2380181 1458690 1429232 29458 0 0.979805 2.282625 1.865564 0 0 0 ? 0 0 0 0 0 0 0 0.496816 284
DUC I34761 5x 0.283048 1437735 864950 845621 19329 0 0.977653 2.314068 1.855518 0 0 0 ? 0 0 0 0 0 0 0 0.487741 314
DUC I34762 5x 0.190719 2113944 1421699 1392593 29106 0 0.979527 2.282196 1.878647 0 0 0 ? 0 0 0 0 0 0 0 0.496752 230
DUC I34763 5x 0.204567 2481696 1522532 1491029 31503 0 0.979309 2.323731 1.927516 0 0 0 ? 0 0 0 0 0 0 0 0.497896 438
DUC I34764 5x 0.225488 1368068 859670 841208 18462 0 0.978524 2.420574 2.048547 0 0 0 ? 0 0 0 0 0 0 0 0.492182 417
DUC I34765 5x 0.156223 2717567 1774821 1739008 35813 0 0.979822 2.291045 1.897492 0 0 0 ? 0 0 0 0 0 0 0 0.504236 532
DUC I34766 5x 0.291870 2446649 1292106 1266144 25962 0 0.979907 2.302479 1.839239 0 0 0 ? 0 0 0 0 0 0 0 0.492352 402
DUC I34767 5x 0.177723 2900952 1780527 1745928 34599 0 0.980568 2.270906 1.872240 0 0 0 ? 0 0 0 0 0 0 0 0.501215 328
DUC I34768 5x 0.165667 2915965 1801284 1764774 36510 0 0.979731 2.304765 1.904073 0 0 0 ? 0 0 0 0 0 0 0 0.503384 579
DUC I34769 5x 0.188868 3715088 1954480 1915500 38980 0 0.980056 2.289276 1.900729 0 0 0 ? 0 0 0 0 0 0 0 0.502915 293
DU6 H07748 30x 0.245382 12466451 2353297 2301866 51431 0 0.978145 2.274999 1.926539 0 0 0 ? 0 0 0 0 0 0 0 0.505848 212
DU6 H07749 30x 0.238745 14716687 2339176 2288809 50367 0 0.978468 2.280116 1.939594 0 0 0 ? 0 0 0 0 0 0 0 0.506193 174
DU6 H07750 30x 0.225888 9682466 2363475 2313691 49784 0 0.978936 2.276579 1.907944 0 0 0 ? 0 0 0 0 0 0 0 0.506560 166
DU6 H07751 30x 0.252863 15194800 2396097 2345572 50525 0 0.978914 2.283294 1.912607 0 0 0 ? 0 0 0 0 0 0 0 0.505198 317
DU6 H07752 30x 0.230168 17419185 2322473 2276453 46020 0 0.980185 2.287482 1.934388 0 0 0 ? 0 0 0 0 0 0 0 0.505947 87
DU6 H07753 30x 0.239785 9965774 2367014 2319198 47816 0 0.979799 2.281460 1.887440 0 0 0 ? 0 0 0 0 0 0 0 0.506690 485
DU6 H07754 30x 0.271358 9542157 2338535 2288220 50315 0 0.978484 2.281026 1.905191 0 0 0 ? 0 0 0 0 0 0 0 0.505452 179
DU6 H07755 30x 0.228145 15571858 2332730 2284657 48073 0 0.979392 2.284035 1.932353 0 0 0 ? 0 0 0 0 0 0 0 0.504514 89
DU6 H07756 30x 0.229069 12658741 2340968 2294004 46964 0 0.979938 2.281245 1.910330 0 0 0 ? 0 0 0 0 0 0 0 0.505878 84
DU6 H07757 30x 0.287141 15198392 2380179 2328356 51823 0 0.978227 2.282986 1.926200 0 0 0 ? 0 0 0 0 0 0 0 0.506138 99
DU6 I34725 5x 0.800817 751285 274657 265469 9188 0 0.966547 2.353109 1.758331 0 0 0 ? 0 0 0 0 0 0 0 0.473941 1622
DU6 I34726 5x 0.448539 2903827 1251147 1221067 30080 0 0.975958 2.290354 1.877643 0 0 0 ? 0 0 0 0 0 0 0 0.487895 569
DU6 I34727 5x 0.733747 992507 382456 370095 12361 0 0.967680 2.351278 1.752394 0 0 0 ? 0 0 0 0 0 0 0 0.478462 1995
DU6 I34728 5x 0.466856 1072937 498448 482584 15864 0 0.968173 2.367836 1.795419 0 0 0 ? 0 0 0 0 0 0 0 0.485159 3340
DU6 I34729 5x 0.365579 2546146 1221349 1192846 28503 0 0.976663 2.326072 1.920689 0 0 0 ? 0 0 0 0 0 0 0 0.490724 901
DU6 I34730 5x 0.361222 2689070 1249576 1219525 30051 0 0.975951 2.332290 1.904320 0 0 0 ? 0 0 0 0 0 0 0 0.493802 1808
DU6 I34731 5x 0.482630 1729918 780480 760382 20098 0 0.974249 2.335097 1.921221 0 0 0 ? 0 0 0 0 0 0 0 0.483195 647
DU6 I34732 5x 0.449463 1431749 667214 650474 16740 0 0.974911 2.353910 1.906755 0 0 0 ? 0 0 0 0 0 0 0 0.481177 702
DU6 I34733 5x 0.840808 1566566 555335 540234 15101 0 0.972807 2.322656 1.870367 0 0 0 ? 0 0 0 0 0 0 0 0.476143 461
DU6 I34734 5x 0.509310 2024090 867722 845862 21860 0 0.974808 2.321078 1.861631 0 0 0 ? 0 0 0 0 0 0 0 0.483141 1094
DU6 I34735 5x 0.566012 2271007 901271 878298 22973 0 0.974510 2.335541 1.901730 0 0 0 ? 0 0 0 0 0 0 0 0.485806 865
DU6 I34736 5x 0.453620 2734717 1165982 1138531 27451 0 0.976457 2.329963 1.918146 0 0 0 ? 0 0 0 0 0 0 0 0.487435 544
DU6 I34737 5x 0.440219 2644235 1175118 1147007 28111 0 0.976078 2.309635 1.885251 0 0 0 ? 0 0 0 0 0 0 0 0.487148 427
DU6 I34738 5x 0.498795 2176913 941278 918411 22867 0 0.975706 2.318858 1.918571 0 0 0 ? 0 0 0 0 0 0 0 0.483594 359
DU6 I34739 5x 0.632703 2025331 778014 757250 20764 0 0.973312 2.339242 1.858087 0 0 0 ? 0 0 0 0 0 0 0 0.482926 1288
DU6P H07768 30x 0.332913 12045910 2350360 2306581 43779 0 0.981373 2.279888 1.887987 0 0 0 ? 0 0 0 0 0 0 0 0.505374 155
DU6P H07769 30x 0.382665 11929963 2387319 2338700 48619 0 0.979634 2.280471 1.930268 0 0 0 ? 0 0 0 0 0 0 0 0.504790 199
DU6P H07770 30x 0.610443 16982973 2438805 2391810 46995 0 0.980730 2.285228 1.905050 0 0 0 ? 0 0 0 0 0 0 0 0.496945 194
DU6P H07771 30x 0.641021 23300704 2501295 2450294 51001 0 0.979610 2.288734 1.930587 0 0 0 ? 0 0 0 0 0 0 0 0.509459 81
DU6P H07772 30x 0.270381 27848116 2161368 2121398 39970 0 0.981507 2.291602 1.971305 0 0 0 ? 0 0 0 0 0 0 0 0.502545 36
DU6P H07773 30x 0.561269 37865170 2483555 2436376 47179 0 0.981003 2.292654 1.932558 0 0 0 ? 0 0 0 0 0 0 0 0.500419 42
DU6P H07774 30x 0.405592 14308906 2328083 2284162 43921 0 0.981134 2.281022 1.863915 0 0 0 ? 0 0 0 0 0 0 0 0.495962 77
DU6P H07775 30x 0.344869 12011639 2335135 2290731 44404 0 0.980984 2.285950 1.893523 0 0 0 ? 0 0 0 0 0 0 0 0.504207 121
DU6P H07776 30x 0.287941 12834776 2300934 2254472 46462 0 0.979807 2.286493 1.954095 0 0 0 ? 0 0 0 0 0 0 0 0.504991 95
DU6P H07777 30x 0.264760 10959458 2296865 2253548 43317 0 0.981141 2.280331 1.895328 0 0 0 ? 0 0 0 0 0 0 0 0.505130 163
DU6P I34740 5x 0.327534 6123723 2113269 2071466 41803 0 0.980219 2.295286 1.931281 0 0 0 ? 0 0 0 0 0 0 0 0.500671 346
DU6P I34741 5x 0.522590 2587111 871818 848133 23685 0 0.972833 2.378881 1.980745 0 0 0 ? 0 0 0 0 0 0 0 0.495123 3224
DU6P I34742 5x 0.352973 6762399 2123070 2081983 41087 0 0.980647 2.312417 1.936674 0 0 0 ? 0 0 0 0 0 0 0 0.501448 542
DU6P I34743 5x 0.306478 5880026 2086024 2046441 39583 0 0.981025 2.302736 1.900278 0 0 0 ? 0 0 0 0 0 0 0 0.501457 359
DU6P I34744 5x 0.302847 6568412 2183664 2139599 44065 0 0.979821 2.300450 1.928880 0 0 0 ? 0 0 0 0 0 0 0 0.502551 342
DU6P I34745 5x 0.392424 4725669 1772629 1738656 33973 0 0.980835 2.314106 1.920399 0 0 0 ? 0 0 0 0 0 0 0 0.496007 399
DU6P I34746 5x 0.330426 5047338 1944832 1906157 38675 0 0.980114 2.307113 1.927263 0 0 0 ? 0 0 0 0 0 0 0 0.497537 399
DU6P I34747 5x 0.369130 4826929 1834071 1796238 37833 0 0.979372 2.291163 1.882075 0 0 0 ? 0 0 0 0 0 0 0 0.496152 412
DU6P I34748 5x 0.381287 5541094 1920762 1881460 39302 0 0.979538 2.316254 1.966636 0 0 0 ? 0 0 0 0 0 0 0 0.497652 1509
DU6P I34749 5x 0.315853 5838801 2033949 1992965 40984 0 0.979850 2.306415 1.953376 0 0 0 ? 0 0 0 0 0 0 0 0.500597 536
DU6P I34750 5x 0.311820 5196313 1964865 1925249 39616 0 0.979838 2.310144 1.909305 0 0 0 ? 0 0 0 0 0 0 0 0.500344 251
DU6P I34751 5x 0.310216 5945974 2108659 2066226 42433 0 0.979877 2.301097 1.932886 0 0 0 ? 0 0 0 0 0 0 0 0.500881 321
DU6P I34752 5x 0.340655 7718048 2255414 2212812 42602 0 0.981111 2.293448 1.902241 0 0 0 ? 0 0 0 0 0 0 0 0.503066 233
DU6P I34753 5x 0.599309 1826196 681507 663338 18169 0 0.973340 2.405680 1.914501 0 0 0 ? 0 0 0 0 0 0 0 0.488677 2721
DU6P I34754 5x 0.318127 8287768 2319638 2276185 43453 0 0.981267 2.287024 1.900541 0 0 0 ? 0 0 0 0 0 0 0 0.502811 206
DUhLB H07778 30x 0.497382 17576553 2434728 2380935 53793 0 0.977906 2.284402 1.936139 0 0 0 ? 0 0 0 0 0 0 0 0.506004 177
DUhLB H07779 30x 0.414630 15858855 2419533 2368206 51327 0 0.978786 2.282837 1.960035 0 0 0 ? 0 0 0 0 0 0 0 0.505811 128
DUhLB H07780 30x 0.470043 26134617 2425902 2372496 53406 0 0.977985 2.288552 1.962063 0 0 0 ? 0 0 0 0 0 0 0 0.505551 132
DUhLB H07781 30x 0.473947 31473031 2418045 2367070 50975 0 0.978919 2.302670 1.982913 0 0 0 ? 0 0 0 0 0 0 0 0.504025 136
DUhLB H07782 30x 0.405033 34101108 2350066 2301568 48498 0 0.979363 2.292178 2.035869 0 0 0 ? 0 0 0 0 0 0 0 0.503567 84
DUhLB H07783 30x 0.416766 26174499 2386651 2333379 53272 0 0.977679 2.289340 1.984593 0 0 0 ? 0 0 0 0 0 0 0 0.505190 115
DUhLB H07784 30x 0.484159 17764891 2372608 2318846 53762 0 0.977341 2.285359 1.937654 0 0 0 ? 0 0 0 0 0 0 0 0.505511 150
DUhLB H07785 30x 0.527376 19625540 2496878 2443601 53277 0 0.978663 2.286376 1.973379 0 0 0 ? 0 0 0 0 0 0 0 0.504537 148
DUhLB H07786 30x 0.451816 13452857 2320048 2271680 48368 0 0.979152 2.296580 1.974845 0 0 0 ? 0 0 0 0 0 0 0 0.504115 1151
DUhLB H07787 30x 0.475214 19259193 2450158 2394702 55456 0 0.977366 2.295288 1.965086 0 0 0 ? 0 0 0 0 0 0 0 0.504866 126
DUhLB I34785 5x 0.497162 7596379 2101915 2057075 44840 0 0.978667 2.301425 2.010810 0 0 0 ? 0 0 0 0 0 0 0 0.499680 441
DUhLB I34786 5x 0.553695 6408395 1864959 1823177 41782 0 0.977596 2.328411 2.018713 0 0 0 ? 0 0 0 0 0 0 0 0.497445 1029
DUhLB I34787 5x 0.551115 5473194 1575252 1539977 35275 0 0.977607 2.353776 1.975538 0 0 0 ? 0 0 0 0 0 0 0 0.497192 1221
DUhLB I34788 5x 0.432537 5547145 1876656 1835174 41482 0 0.977896 2.322731 2.014461 0 0 0 ? 0 0 0 0 0 0 0 0.497235 571
DUhLB I34789 5x 0.534553 7944292 1942831 1898972 43859 0 0.977425 2.337397 2.003424 0 0 0 ? 0 0 0 0 0 0 0 0.499701 902
DUhLB I34790 5x 0.491587 7766995 2105697 2058687 47010 0 0.977675 2.305917 1.977955 0 0 0 ? 0 0 0 0 0 0 0 0.499126 291
DUhLB I34791 5x 0.495271 6393317 1871825 1828164 43661 0 0.976675 2.330644 2.020059 0 0 0 ? 0 0 0 0 0 0 0 0.498930 1061
DUhLB I34792 5x 0.493844 6735102 1977983 1933735 44248 0 0.977630 2.316847 1.979262 0 0 0 ? 0 0 0 0 0 0 0 0.499141 475
DUhLB I34793 5x 0.455535 10612345 2351304 2300000 51304 0 0.978181 2.299445 1.969669 0 0 0 ? 0 0 0 0 0 0 0 0.503055 811
DUhLB I34794 5x 0.510819 5372890 1611331 1573160 38171 0 0.976311 2.356533 2.029204 0 0 0 ? 0 0 0 0 0 0 0 0.497576 1092
DUhLB I34795 5x 0.551171 9688139 2268645 2220406 48239 0 0.978737 2.304859 1.954011 0 0 0 ? 0 0 0 0 0 0 0 0.501528 429
DUhLB I34796 5x 0.529655 8182201 2104028 2055745 48283 0 0.977052 2.314066 1.983010 0 0 0 ? 0 0 0 0 0 0 0 0.500407 943
DUhLB I34797 5x 0.533709 7003741 1891356 1846341 45015 0 0.976200 2.330671 1.979547 0 0 0 ? 0 0 0 0 0 0 0 0.499537 1055
DUhLB I34798 5x 0.449878 7812860 2096205 2048419 47786 0 0.977204 2.308582 1.971027 0 0 0 ? 0 0 0 0 0 0 0 0.501804 602
DUhLB I34799 5x 0.542204 6326728 1880285 1837180 43105 0 0.977075 2.313655 1.959086 0 0 0 ? 0 0 0 0 0 0 0 0.497776 615
FZTDU H07738 30x 1.187596 51164568 2781961 2718004 63957 0 0.977010 2.280910 1.955636 0 0 0 ? 0 0 0 0 0 0 0 0.504278 1362
FZTDU H07739 30x 1.085203 29317382 2828714 2765079 63635 0 0.977504 2.285940 1.928844 0 0 0 ? 0 0 0 0 0 0 0 0.503960 2146
FZTDU H07740 30x 1.167723 30091426 2708908 2649467 59441 0 0.978057 2.279149 1.934344 0 0 0 ? 0 0 0 0 0 0 0 0.503433 513
FZTDU H07741 30x 1.067012 34542761 2739458 2679769 59689 0 0.978211 2.287435 1.993430 0 0 0 ? 0 0 0 0 0 0 0 0.503735 608
FZTDU H07742 30x 1.121631 36750210 2837062 2773471 63591 0 0.977586 2.287014 1.988158 0 0 0 ? 0 0 0 0 0 0 0 0.503951 2285
FZTDU H07743 30x 1.041063 44010614 2743999 2687949 56050 0 0.979574 2.287311 1.922772 0 0 0 ? 0 0 0 0 0 0 0 0.503867 531
FZTDU H07744 30x 1.036236 42901972 2707721 2647072 60649 0 0.977601 2.295362 1.979124 0 0 0 ? 0 0 0 0 0 0 0 0.503917 1957
FZTDU H07745 30x 1.114108 44995318 2792910 2734180 58730 0 0.978972 2.285599 1.913339 0 0 0 ? 0 0 0 0 0 0 0 0.503329 862
FZTDU H07746 30x 1.172747 37926745 2689220 2628023 61197 0 0.977244 2.282313 1.953808 0 0 0 ? 0 0 0 0 0 0 0 0.503616 876
FZTDU H07747 30x 1.071563 40349413 2780317 2720810 59507 0 0.978597 2.284800 1.938762 0 0 0 ? 0 0 0 0 0 0 0 0.502662 2295
FZTDU I34710 5x 1.123016 22279573 2672149 2614169 57980 0 0.978302 2.292682 1.940759 0 0 0 ? 0 0 0 0 0 0 0 0.502780 356
FZTDU I34711 5x 1.182405 13912971 2242753 2189946 52807 0 0.976454 2.317457 2.004666 0 0 0 ? 0 0 0 0 0 0 0 0.498301 950
FZTDU I34712 5x 1.383420 16377031 2252718 2202746 49972 0 0.977817 2.349430 1.971164 0 0 0 ? 0 0 0 0 0 0 0 0.499820 1124
FZTDU I34713 5x 1.027019 20878493 2710676 2650705 59971 0 0.977876 2.290733 1.946399 0 0 0 ? 0 0 0 0 0 0 0 0.503402 1401
FZTDU I34714 5x 1.108162 16164092 2528424 2469593 58831 0 0.976732 2.301074 1.949218 0 0 0 ? 0 0 0 0 0 0 0 0.500143 676
FZTDU I34715 5x 1.092839 18908999 2573407 2515300 58107 0 0.977420 2.302752 1.945109 0 0 0 ? 0 0 0 0 0 0 0 0.501733 922
FZTDU I34716 5x 1.220399 17396787 2184910 2135418 49492 0 0.977348 2.336836 1.981087 0 0 0 ? 0 0 0 0 0 0 0 0.500941 1483
FZTDU I34717 5x 1.236633 16695940 2025763 1981208 44555 0 0.978006 2.347608 1.950467 0 0 0 ? 0 0 0 0 0 0 0 0.500150 1726
FZTDU I34718 5x 1.060945 17940114 2593648 2534516 59132 0 0.977201 2.300856 1.955418 0 0 0 ? 0 0 0 0 0 0 0 0.502280 565
FZTDU I34719 5x 1.248269 11625591 2201611 2151585 50026 0 0.977278 2.307749 1.962222 0 0 0 ? 0 0 0 0 0 0 0 0.497433 917
FZTDU I34720 5x 1.183226 22034130 2721252 2661878 59374 0 0.978181 2.292382 1.927568 0 0 0 ? 0 0 0 0 0 0 0 0.503291 1642
FZTDU I34721 5x 1.277354 11341427 2162869 2113788 49081 0 0.977307 2.306638 1.984918 0 0 0 ? 0 0 0 0 0 0 0 0.496083 1429
FZTDU I34722 5x 1.109965 20108220 2572889 2515445 57444 0 0.977673 2.287751 1.954027 0 0 0 ? 0 0 0 0 0 0 0 0.502527 729
FZTDU I34723 5x 1.511955 14254984 1995876 1949815 46061 0 0.976922 2.354907 1.945830 0 0 0 ? 0 0 0 0 0 0 0 0.500148 3205
FZTDU I34724 5x 1.279576 11208255 2173804 2124379 49425 0 0.977263 2.313321 1.979743 0 0 0 ? 0 0 0 0 0 0 0 0.496288 2552

Population metrics

Population VCFs were produced from cohort final-VCF by extracting samples and removing fixed reference sites (GT==“RR”) and all-missing sites (GT==“./.”).